How To Tell If Bed/Bim/Fam Data Are Phased?

For VCF files the rule is "pipe means phased, slash unphased". See A: Phased and unphased genotypes in VCF files: does the order of alleles matter?

Is there such a rule for the bed/bim/fam family of files?

bed

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updated 12.8 years ago by zx8754

• written 12.8 years ago by Click downvote

1 answer

As far as I know, bed/bim/fam is a plink binary format of regular ped/map format, which is not a phased format.

See SHAPEIT for examples of file formats.

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written 12.8 years ago by zx8754

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